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Messages - Dongzhe

Pages: [1] 2
1
General Questions and Answers / LDA+U in noncollinear spin
« on: April 8, 2024, 16:53 »
Dear ATK experts,

In QuantumATK-V-2023.12, is it possible to model LDA+U with noncollinear spins?

Thanks,
Best regards,
Dongzhe (CNRS, France)

2
General Questions and Answers / Re: Phonon spectrum error
« on: February 13, 2024, 09:43 »
Thanks for your kind help, it is indeed working with the newest version.
Best regards,
Dongzhe (CNRS, France)

3
General Questions and Answers / Re: Phonon spectrum error
« on: January 25, 2024, 08:56 »
Dear Anders,

I tested with another geometry with fractional 0.3 in the z direction, I ended up with the same error. The dynamical matrix part is finished without problems, but it gets an error for the Phonon band.

Previously, I also tested the silicon tutorial with no problems.

+------------------------------------------------------------------------------+
| Executing task 25 / 25:                                                      |
|   Generate dynamical matrix from displaced forces                            |
|   Log to: stdout                                                             |
+------------------------------------------------------------------------------+
Master    : Handling exception in delegator process.
  Traceback (most recent call last):
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 427, in __runInParallelModeAsDelegator
    File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 1323, in schedulerCode
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 704, in waitAllTasksFinished
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 1075, in __processTask
  NL.ComputerScienceUtilities.ParallelTools.DynamicTaskScheduler.TaskExecutionError: An exception was raised while executing task "20a64c4cba8711ee95c4080038b56a4d".
    Traceback (most recent call last):
      File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 1309, in __startParallelExecutionOnWorkerProcesses
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 1081, in _runTask
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 619, in run
      File "zipdir/NL/Study/DynamicalMatrixTasks.py", line 940, in _execute
      File "zipdir/NL/Study/DynamicalMatrixTasks.py", line 1031, in _applySymmetries
      File "zipdir/NL/Study/DynamicalMatrixTasks.py", line 1072, in getBlock
      File "zipdir/NLEngine.py", line 21582, in get
    RuntimeError:
    ** Back Engine Exception : Column index out of bounds
    ** Location of Exception : sparsematrix.h:140

Is it a bug for magnetic systems?

Best regards,
Dongzhe (CNRS, France)

4
General Questions and Answers / Re: Phonon spectrum error
« on: January 22, 2024, 11:08 »
Dear Anders,
Thanks for your reply.
I used "QuantumATK-T-2022.03".
You can download the hdf5 and input/output files of my calculation using the following link:
https://filesender.renater.fr/?s=download&token=9fdc8987-6eb5-4c5d-b846-fb4934f78f64
BTW, I used sufficiently large RAM.
Best regards,
Dongzhe (CNRS, France)

5
General Questions and Answers / Re: Phonon spectrum error
« on: January 16, 2024, 06:55 »
Dear,

This is the error message (just before the phonon band structure, after the calculation of the dynamical matrix):

-------------------------------------------------------------------------------------------------------------
Master    : Handling exception in delegator process.
  Traceback (most recent call last):
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 427, in __runInParallelModeAsDelegator
    File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 1323, in schedulerCode
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 704, in waitAllTasksFinished
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 1075, in __processTask
  NL.ComputerScienceUtilities.ParallelTools.DynamicTaskScheduler.TaskExecutionError: An exception was raised while executing task "e64ae6a4a4e511ee92db080038b56985".
    Traceback (most recent call last):
      File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 1309, in __startParallelExecutionOnWorkerProcesses
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 1081, in _runTask
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 619, in run
      File "zipdir/NL/Study/DynamicalMatrixTasks.py", line 940, in _execute
      File "zipdir/NL/Study/DynamicalMatrixTasks.py", line 1031, in _applySymmetries
      File "zipdir/NL/Study/DynamicalMatrixTasks.py", line 1072, in getBlock
      File "zipdir/NLEngine.py", line 21582, in get
    RuntimeError:
    ** Back Engine Exception : Column index out of bounds
    ** Location of Exception : sparsematrix.h:140
-------------------------------------------------------------------------------------------------------------------------------------------

6
General Questions and Answers / Re: Phonon spectrum error
« on: January 3, 2024, 07:58 »
Dear again,

My input file is attached:


# -*- coding: utf-8 -*-
# -------------------------------------------------------------
# Bulk Configuration
# -------------------------------------------------------------

# Set up lattice
lattice = Hexagonal(4.000000017612248*Angstrom, 30.000000132091856*Angstrom)

# Define elements
elements = [Tellurium, Iron, Germanium, Iron, Iron, Tellurium]

# Define coordinates
fractional_coordinates = [[ 0.333333331756, -0.333333331756,  0.086864976284],
                          [ 0.            ,  0.            ,  0.041338246485],
                          [-0.333333331756,  0.333333331756,  0.            ],
                          [ 0.333333331756, -0.333333331756,  0.            ],
                          [ 0.            ,  0.            , -0.041338246485],
                          [ 0.333333331756, -0.333333331756, -0.086864976284]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = SGGA.PBE

k_point_sampling = MonkhorstPackGrid(
    na=12,
    nb=12,
    )
numerical_accuracy_parameters = NumericalAccuracyParameters(
    density_mesh_cutoff=150.0*Hartree,
    k_point_sampling=k_point_sampling,
    occupation_method=FermiDirac(300.0*Kelvin*boltzmann_constant),
    )

iteration_control_parameters = IterationControlParameters(
    tolerance=1e-05,
    max_steps=300,
    )

calculator = LCAOCalculator(
    exchange_correlation=exchange_correlation,
    numerical_accuracy_parameters=numerical_accuracy_parameters,
    iteration_control_parameters=iteration_control_parameters,
    )

bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('analysis.hdf5', bulk_configuration)

# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
bulk_configuration = OptimizeGeometry(
    bulk_configuration,
    max_forces=0.01*eV/Ang,
    max_steps=300,
    max_step_length=0.2*Ang,
    trajectory_filename='analysis_trajectory.hdf5',
    trajectory_interval=5.0*Minute,
    restart_strategy=RestartFromTrajectory(),
    disable_stress=True,
    optimizer_method=LBFGS(),
    enable_optimization_stop_file=True,
)
nlsave('analysis.hdf5', bulk_configuration)
nlprint(bulk_configuration)

# -------------------------------------------------------------
# Dynamical Matrix
# -------------------------------------------------------------
dynamical_matrix = DynamicalMatrix(
    bulk_configuration,
    filename='analysis.hdf5',
    object_id='dynamical_matrix',
    repetitions=(7, 7, 1),
    atomic_displacement=0.01*Angstrom,
    acoustic_sum_rule=True,
    finite_difference_method=Central,
    force_tolerance=1e-09*Hartree/Bohr**2,
    processes_per_displacement=None,
    log_filename_prefix='forces_displacement_',
    use_wigner_seitz_scheme=True,
    )
dynamical_matrix.update()

# -------------------------------------------------------------
# Phonon Bandstructure
# -------------------------------------------------------------
phonon_bandstructure = PhononBandstructure(
    configuration=bulk_configuration,
    dynamical_matrix=dynamical_matrix,
    route=['G', 'K', 'M', 'G'],
    points_per_segment=400,
    number_of_bands=All
    )
nlsave('analysis.hdf5', phonon_bandstructure)

The calculation for the dynamical matrix has been finished properly, but I got an error in plotting bands.

Best regards,
Dongzhe (CNRS, France)


7
General Questions and Answers / Phonon spectrum error
« on: December 28, 2023, 11:08 »
Dear ATK experts,

I have been using QuantumATK-T-2022.03 for the calculation of the Phonon band structure. I used 10 nodes.

The calculation of the dynamical matrix was done properly, then I got the following error:

-------------------------------------------------------------------------------------------------------------------------------------------

+------------------------------------------------------------------------------+
| Executing task 24 / 25:                                                      |
|   Force calculation                                                          |
|   Atom index: 0                                                              |
|   Displacement direction: +x                                                 |
|   Log to: forces_displacement_0_plus_x.log                                   |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Executing task 25 / 25:                                                      |
|   Generate dynamical matrix from displaced forces                            |
|   Log to: stdout                                                             |
+------------------------------------------------------------------------------+
Master    : Handling exception in delegator process.
  Traceback (most recent call last):
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 427, in __runInParallelModeAsDelegator
    File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 1323, in schedulerCode
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 704, in waitAllTasksFinished
    File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 1075, in __processTask
  NL.ComputerScienceUtilities.ParallelTools.DynamicTaskScheduler.TaskExecutionError: An exception was raised while executing task "e64ae6a4a4e511ee92db080038b56985".
    Traceback (most recent call last):
      File "zipdir/NL/ComputerScienceUtilities/ParallelTools/DynamicTaskScheduler.py", line 1309, in __startParallelExecutionOnWorkerProcesses
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 1081, in _runTask
      File "zipdir/NL/ComputerScienceUtilities/Workflow/Workflow.py", line 619, in run
      File "zipdir/NL/Study/DynamicalMatrixTasks.py", line 940, in _execute
      File "zipdir/NL/Study/DynamicalMatrixTasks.py", line 1031, in _applySymmetries
      File "zipdir/NL/Study/DynamicalMatrixTasks.py", line 1072, in getBlock
      File "zipdir/NLEngine.py", line 21582, in get
    RuntimeError:
    ** Back Engine Exception : Column index out of bounds
    ** Location of Exception : sparsematrix.h:140
-------------------------------------------------------------------------------------------------------------------------------------------

Do you have any thoughts on what might be causing the error?
Thanks,
Best regards,
Dongzhe Li (CNRS, France)

8
Installation and License Questions / Re: U-2022.12-SP1 installation problem
« on: June 29, 2023, 14:31 »
Dear,
OK, thanks, it is indeed working.

I have been using the following line for other ATK versions without any problems.
mpiexec -np 1 atkpython < test.py >> test.out

It makes only problems for "U-2022.12-SP1"...

Any further explication?
Best regards,
Dongzhe

9
Installation and License Questions / Re: U-2022.12-SP1 installation problem
« on: June 29, 2023, 10:35 »
Dear Anders,
I have tried using the MPI library from QATK (see below).
However, I am facing the same problem. The job was completed without errors, but it did not calculate anything...
Any further suggestions?
Thanks,
Dongzhe
CNRS in Toulouse

------------------------------------------------------------------------
#var environnements
export OMP_NUM_THREADS=1

#export I_MPI_DAPL_TRANSLATION_CACHE=0
export PATH=/usr/local/QuantumATK/QuantumATK-U-2022.12-SP1/bin:$PATH
export MPILIB=/usr/local/QuantumATK/QuantumATK-U-2022.12-SP1/mpi/lib
export MPIBIN=/usr/local/QuantumATK/QuantumATK-U-2022.12-SP1/mpi/bin

export PATH=$MPIBIN:$PATH
export LD_LIBRARY_PATH=$MPILIB:$LD_LIBRARY_PATH

which mpiexec

echo Time is `date`
echo Directory is `pwd`
date
which atkpython

mpiexec -np 1 atkpython < test.py >> test.out
------------------------------------------------------------------------

10
Installation and License Questions / Re: U-2022.12-SP1 installation problem
« on: June 26, 2023, 14:11 »
Dear,
I have set the same environment (intelmpi/18.2) for older versions of ATK.
I only have problems with U-2022.12-SP1.
Best regards,
Dongzhe

11
Installation and License Questions / Re: U-2022.12-SP1 installation problem
« on: June 13, 2023, 11:46 »
It was installed in a cluster (linux).
Best regards,
Dongzhe

12
Installation and License Questions / U-2022.12-SP1 installation problem
« on: June 11, 2023, 13:44 »
Dear QATK developers,
 
I hold a license through the Europractice program. Recently I installed the newest version of QATK, but I cannot run "atkpython", I always get the following message without errors (see below).

In contrast, I can use the graphical interface using "quantumatk", meaning nothing related to the license issue.

Any comments?

Thanks in advance,

Dongzhe
CNRS in Toulouse, France

+------------------------------------------------------------------------------+
|                                                                              |
|                                  QuantumATK®                                 |
|                                                                              |
|        Version: U-2022.12-SP1 for Windows and Linux [Build da6f78d527]       |
|                                                                              |
|                      Copyright © 2004-2023 Synopsys, Inc.                    |
|                                                                              |
|       This software and all associated documentation are proprietary to      |
|         Synopsys, Inc. This software may only be used pursuant to the        |
|       terms and conditions of a written license agreement with Synopsys,     |
|       Inc. All other use, reproduction, modification, or distribution of     |
|                     this software is strictly prohibited.                    |
|                                                                              |
+------------------------------------------------------------------------------+

Timing:                          Total     Per Step        %

--------------------------------------------------------------------------------

Loading Modules + MPI   :      10.14 s      10.14 s      99.99% |=============|
--------------------------------------------------------------------------------
Total                   :      10.14 s

13
General Questions and Answers / Re: Strange results in Te (Tellurium) atom
« on: August 15, 2022, 07:57 »
Hi,

There are two things that might be important:
1. Your results depend on your DFT Hamiltonian (basis sets, functional, DFT+U...). So, better to first check whether you can reproduce well the band structure of VTe2 compared to the literature.
2. The methodology for calculating the HeisenbergExchange constant might be different. The QATK uses Green's function approach which treats the spin rotation as a perturbation. There are also other methods such as the spin spiral approach (based on the generalized Bloch theorem) and the supercell approach, often used in the literature. Different methods can probably give different results. However, in many cases, we expect to have a qualitative agreement.

Best regards,
Dongzhe

14
General Questions and Answers / Re: Density of states of a specific spin state
« on: August 15, 2022, 07:45 »
Hi,
You need something like this:

# read the dos
dos = nlread('../xxx.hdf5',DeviceDensityOfStates)[0]
energies = dos.energies()

dos_up = dos.evaluate(spin=Spin.Up, projection_list = ProjectionList(atoms=All))
dos_down = dos.evaluate(spin=Spin.Down, projection_list = ProjectionList(atoms=All))

Have a look at the tutorial:
https://docs.quantumatk.com/manual/Types/DeviceDensityOfStates/DeviceDensityOfStates.html

Best,
Dongzhe Li
CEMES-CNRS, France

15
General Questions and Answers / Re: GGA+U
« on: April 21, 2022, 06:13 »
Hi,
Have u compared your GGA+U band structure to the literature? There are several different ways for DFT+U methodology. So, in principle, you can not take one U value from the literature and then perform QATK calculations with the same U.
Best,
Dongzhe Li

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